OpenMS
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The LabeledPairFinder allows the matching of labeled features (features with a fixed distance). More...
#include <OpenMS/ANALYSIS/MAPMATCHING/LabeledPairFinder.h>
Public Member Functions | |
LabeledPairFinder () | |
Default constructor. More... | |
~LabeledPairFinder () override | |
Destructor. More... | |
void | run (const std::vector< ConsensusMap > &input_maps, ConsensusMap &result_map) override |
Run the algorithm. More... | |
Public Member Functions inherited from BaseGroupFinder | |
BaseGroupFinder () | |
Default constructor. More... | |
~BaseGroupFinder () override | |
Destructor. More... | |
Public Member Functions inherited from DefaultParamHandler | |
DefaultParamHandler (const String &name) | |
Constructor with name that is displayed in error messages. More... | |
DefaultParamHandler (const DefaultParamHandler &rhs) | |
Copy constructor. More... | |
virtual | ~DefaultParamHandler () |
Destructor. More... | |
DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () const |
Non-mutable access to the name. More... | |
void | setName (const String &name) |
Mutable access to the name. More... | |
const std::vector< String > & | getSubsections () const |
Non-mutable access to the registered subsections. More... | |
Public Member Functions inherited from ProgressLogger | |
ProgressLogger () | |
Constructor. More... | |
virtual | ~ProgressLogger () |
Destructor. More... | |
ProgressLogger (const ProgressLogger &other) | |
Copy constructor. More... | |
ProgressLogger & | operator= (const ProgressLogger &other) |
Assignment Operator. More... | |
void | setLogType (LogType type) const |
Sets the progress log that should be used. The default type is NONE! More... | |
LogType | getLogType () const |
Returns the type of progress log being used. More... | |
void | setLogger (ProgressLoggerImpl *logger) |
Sets the logger to be used for progress logging. More... | |
void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
Initializes the progress display. More... | |
void | setProgress (SignedSize value) const |
Sets the current progress. More... | |
void | endProgress (UInt64 bytes_processed=0) const |
void | nextProgress () const |
increment progress by 1 (according to range begin-end) More... | |
Protected Member Functions | |
double | PValue_ (double x, double m, double sig1, double sig2) |
return the p-value at position x for the bi-Gaussian distribution with mean m and standard deviation sig1 (left) and sig2 (right) More... | |
Protected Member Functions inherited from BaseGroupFinder | |
void | checkIds_ (const std::vector< ConsensusMap > &maps) const |
Checks if all file descriptions have disjoint map identifiers. More... | |
Protected Member Functions inherited from DefaultParamHandler | |
virtual void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Private Member Functions | |
LabeledPairFinder (const LabeledPairFinder &source) | |
Copy constructor not implemented => private. More... | |
LabeledPairFinder & | operator= (const LabeledPairFinder &source) |
Assignment operator not implemented => private. More... | |
Additional Inherited Members | |
Public Types inherited from ProgressLogger | |
enum | LogType { CMD , GUI , NONE } |
Possible log types. More... | |
Static Public Member Functions inherited from DefaultParamHandler | |
static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") |
Writes all parameters to meta values. More... | |
Protected Attributes inherited from DefaultParamHandler | |
Param | param_ |
Container for current parameters. More... | |
Param | defaults_ |
Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
std::vector< String > | subsections_ |
Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
String | error_name_ |
Name that is displayed in error messages during the parameter checking. More... | |
bool | check_defaults_ |
If this member is set to false no checking if parameters in done;. More... | |
bool | warn_empty_defaults_ |
If this member is set to false no warning is emitted when defaults are empty;. More... | |
Protected Attributes inherited from ProgressLogger | |
LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
Static Protected Attributes inherited from ProgressLogger | |
static int | recursion_depth_ |
The LabeledPairFinder allows the matching of labeled features (features with a fixed distance).
Finds feature pairs that have a defined distance in RT and m/z in the same map.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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rt_estimate | string | true | true, false | If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance. Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance. |
rt_pair_dist | float | -20.0 | optimal pair distance in RT [sec] from light to heavy feature | |
rt_dev_low | float | 15.0 | min: 0.0 | maximum allowed deviation below optimal retention time distance |
rt_dev_high | float | 15.0 | min: 0.0 | maximum allowed deviation above optimal retention time distance |
mz_pair_dists | float list | [4.0] | optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge) | |
mz_dev | float | 0.05 | min: 0.0 | maximum allowed deviation from optimal m/z distance |
mrm | string | false | true, false | this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account) |
Implement support for labeled MRM experiments, Q1 m/z value and charges. (Andreas)
Implement support for more than one mass delta, e.g. from missed cleavages and so on (Andreas)
Default constructor.
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inlineoverride |
Destructor.
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private |
Copy constructor not implemented => private.
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private |
Assignment operator not implemented => private.
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inlineprotected |
return the p-value at position x for the bi-Gaussian distribution with mean m
and standard deviation sig1
(left) and sig2
(right)
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overridevirtual |
Run the algorithm.
Exception::IllegalArgument | is thrown if the input data is not valid. |
Implements BaseGroupFinder.